C API 1.0.0

This major release marks the point at which the documented API becomes stable and supported.

Breaking changes

• Change the type of genotypes to int32_t, removing the TSK_16_BIT_GENOTYPES flag option.
  (@benjeffery, #463, #2108)

• tsk_variant_t now includes its tsk_site_t rather than pointing to it.
  (@benjeffery, #2161, #2162)

• Rename TSK_TAKE_TABLES to TSK_TAKE_OWNERSHIP.
  (@benjeffery, #2221, #2222)

• TSK_DEBUG, TSK_NO_INIT, TSK_NO_CHECK_INTEGRITY and TSK_TAKE_OWNERSHIP have moved to core.h
  (@benjeffery, #2218, #2230))

• Rename several flags:

  • All flags to simplify for example TSK_KEEP_INPUT_ROOTS becomes TSK_SIMPLIFY_KEEP_INPUT_ROOTS.
  • All flags to subset for example TSK_KEEP_UNREFERENCED becomes TSK_SUBSET_KEEP_UNREFERENCED.
  • TSK_BUILD_INDEXES -> TSK_TS_INIT_BUILD_INDEXES
  • TSK_NO_METADATA -> TSK_TABLE_NO_METADATA
  • TSK_NO_EDGE_METADATA -> TSK_TC_NO_EDGE_METADATA

  (@benjeffery, #1720, #2226, #2229, #2224)

• Remove the generic TSK_ERR_OUT_OF_BOUNDS - replacing with specific errors.
  Remove TSK_ERR_NON_SINGLE_CHAR_MUTATION which was unused.
  (@benjeffery, #2260)

• Reorder stats API methods to place result as the last argument. (@benjeffery, #2292, #2285)

Features

• Make dumping of tables and tree sequences to disk a zero-copy operation.
  (@benjeffery, #2111, #2124)

• Add edge attribute to mutation_t struct and make available in tree sequence.
  (@jeromekelleher, #685, #2279)

• Reduce peak memory usage in tsk_treeseq_simplify.
  (@jeromekelleher, #2287, #2288)